MIRA Summary Report

tiny_test_run_flu_illumina



Barcode Assignment

The ideal result would be a similar number of reads assigned to each test and positive control. However, it is ok to not have similar read numbers per sample. Samples with a low proportion of reads may indicate higher Ct of starting material or less performant PCR during library preparation. What is most important for sequencing assembly is raw count of reads and their quality.

Automatic Quality Control Decisions

MIRA requires a minimum median coverage of 50x, a minimum coverage of the reference length of 90%, and less than 10 minor variants >=5%. These are marked in yellow to orange according to the number of these failure types. Samples that failed to generate any assembly are marked in red. In addition, premature stop codons are flagged in yellow. CDC does not submit sequences with premature stop codons, particularly in HA, NA or SARS-CoV-2 Spike. Outside of those genes, premature stop codons near the end of the gene may be ok for submission. Hover your mouse over the figure to see individual results.

Median Coverage

The heatmap summarizes the mean coverage per sample per reference.

MIRA Summary Table

Download excel

Individual Sample Coverage Figures

sample_1
sample_3
sample_2
sample_4

AA Variants Table

Download excel

Minor Table Download

Download minor variants table
Download minor indels table

Fasta downloads

(Right-click->"Save link as...")

amino_acid_consensus.fasta

failed_amended_consensus.fasta

failed_amino_acid_consensus.fasta

amended_consensus.fasta